I guess it's plausible to damage the crank sensor while replacing the compensator but you'd have to be really careless about it lol. I definitely agree though, the crank sensor would be what tells the coils to fire
I was thinking more about the harness/wiring going to the crank sensor, since he's already eliminated it by testing on his buddy's bike.
Here's the thing, I'm basically playing a mental game of 'What is the best/easiest/only way to fuck this up...if I was trying to?' ...While using only the information given in the story.
No mention has been made of any DTC's, so either there are none, or it just hasn't been checked yet - Clarifying that would help us, help him, a lot (hint to OP..).
So problem area 1:
He changed the compensator, but no mention was made of how much disassembly was done to get that accomplished, so if we take the liberty of assuming the worse ...(solely for diagnostic purposes)... The the wiring could potentially have been exposed to a bit of tug/pinch/pull.
His ckp sensor worked on his buddy's bike but not his. Could the wiring going to it have peen pulled, strained, pinched ... Or as Thermo put it "Murphy'ed"? Under the circumstances, it's damn sure worth exploring to see if a pin backed out, etc..
Problem area 2:
He mentioned that there was power at the coil on the Y/GN wire, and that the plugs were wet. Since they are - according to the wiring diagram - powered by the same wire/conductor path - Chances are good that the problem isn't there.
His coil worked on his buddy's bike, but not on his. So if he tested the power "with a probe" are we talking about the classic old school - stab into the wire with a test light - style probe? That wouldn't tell us if the wires got pulled out of the plug...just enough.
The battery is heavy and it's a bit awkward getting it in-and-out the first few times. So if it managed to slip and drop in on the wiring, it could - conceivably - have tugged on the coil wires just enough to back out a pin - and the probe test could easily miss that.
Then there is the ECM, was it disconnected during the replacement, or just tucked off to the side - Either way, how well is its connectors seated now?
To be honest, my money is on option 2 ...(pin on coil plug backed out)... Because that really is about the easiest way to end up here that I can think of.